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Bold thinking leads to solving the unsolvable. 

Garvan scientists have long known that there is a myriad of genetic diseases that are difficult to diagnose because they exist on DNA sequences that are too long to read.

Current processes have struggled to accurately diagnose these genetic diseases, known as repeat expansion disorders. Standard methods are costly - they require huge computers, months of processing and can only test for one disorder at a time.

But the difficulty, or absence of methodology, has never stopped us. Solving the unsolvable is what we are here to do.

Dr Ira Deveson, Genomic Technologies Head, and his team, have created a methodology to read previously unreadable sequences of DNA - opening up the possibility to diagnose many previously hidden genetic diseases.

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Dr Ira Deveson
Dr Ira Deveson

In the last five years, next generation sequencing data and analysis has uncovered over 50 new tandem repeat expansion disorders, caused by a stutter in the patient’s genetic code. But they present a huge challenge for current testing methods: put simply, short-read sequencing techniques find it hard to resolve these sequences, because they are too long for the machine to read.

Standard testing can only tackle each sequence one at a time, which has meant analysing the data is complex and time consuming.

Dr Ira Deveson and his team decided to tackle the challenge with a novel solution: building a nanopore long-read sequencing method that can analyse all 50 tandem repeat expansion disorders across approximately 50 genes at the same time.

Many genetic diseases sit on sequences of DNA that are too long to be read.

DNA sequence

This means that many diseases remain unsolved, leaving countless people without a diagnosis. Our team at Garvan, led by Dr Ira Deveson, has come up with a groundbreaking solution.

Nanopore technology has historically been seen as too error-prone and the process to get an accurate consensus of all the reads has historically been quite slow and computationally intensive. To resolve this problem, Dr Deveson and his team of scientists, computer analysts and engineers developed a sophisticated methodology that effectively takes this process and miniaturises it. Where it would usually require a super-computer the size of a room to process the data, it can now be delivered on a handheld device, or even a smart phone.

 

Dr Ira Deveson on our bold new approach to diagnosis

Our breakthrough technique not only accurately reads the tandem repeat expansion and diagnoses the disorder, but does it much faster and more cost-effectively than current sequencing methods.

Nanopore technology has historically been seen as too error-prone and the process to get an accurate consensus of all the reads has historically been quite slow and computationally intensive. To resolve this problem, Dr Deveson and his team of scientists, computer analysts and engineers developed a sophisticated methodology that effectively takes this process and miniaturises it. Where it would usually require a super-computer the size of a room to process the data, it can now be delivered on a handheld device, or even a smart phone.

Our breakthrough technique not only accurately reads the tandem repeat expansion and diagnoses the disorder, but does it much faster and more cost-effectively than current sequencing methods.

“There are so many applications – it’s all DNA to us.” – Dr Ira Deveson

Your support for work like Dr Deveson’s opens up immense possibilities to help diagnose these unsolved cases. Together, we can resolve the diagnoses for countless people who live in limbo, unable to access accurate information about their disease progression and occurrence.

Patients and their families often wait months or years for a clear diagnosis. In fact, 50-70% of genetic diseases currently go without a diagnosis. This breakthrough can put an end to the diagnostic odyssey for people living with repeat expansion diseases.

Dr Kishore Kumar

Clinical neurologist and visiting scientist Dr Kishore Kumar is witnessing first-hand the impact of Dr Deveson’s groundbreaking work.

Dr Kumar is partnering with Garvan to bring Dr Deveson’s new method from the lab to patients like John, who has cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS). CANVAS is a rare genetic disorder distinguished by a debilitating loss of coordination and balance. It was only recently discovered to be caused by an expansion in the RFC1 gene – one of the genes Dr Deveson’s work can now analyse as part of a panel.

“Many patients I see have never known what the cause of their problem is, so a diagnosis in itself can have such a profound effect.” – Dr Kishore Kumar

One of Dr Kumar’s patients, John, diagnosed with CANVAS

For John, understanding the genetic cause of his symptoms helped him and his family make choices about what was important to them. It gave his children crucial knowledge about the possibility of an inherited condition that may affect their own life plans. It’s also helped John access support, including a physiotherapist who specialises in neurological conditions and is working with him to manage his physical disabilities.

Importantly, John’s diagnosis may one day help connect him with clinical trials that are searching for answers for his disease.